How To Normalize Sequencing Coverage For Aneuploid Samples?

Question

[Christian]

In order to facilitate matched tumor/normal comparisons. Simply dividing by the total number of reads does not work well because of different chromosome numbers.

[Christian]

I should add that I am interested in cnv detection, not gene expression analysis.

Answer 1

[Abhi]

Good point..never thought about this but then I dont work with tumor/normal cancer samples. The following might be useful watch.

In one of the recent talk by Lior Pachter he recommends using TPM method for counting against the more common idea of RPKM and FPKM and I think he does a great job of explaining statistically why this is so.

In summary in RPKM/FPKM model we assume an important factor as constant, total abundance of all the transcripts for the sample but that varies across the samples/experiments and thus needed to be factored while counting abundance of each transcript across samples.

Hope this helps, -Abhi